|
| Status |
Public on Jul 28, 2020 |
| Title |
G4_d4_Cy5-PDS_1uM_plus_3uM_BMVC_comp_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
1uM Cy5-PDS + 3uM BMVC, G4 design 4
|
| Organism |
synthetic construct |
| Characteristics |
molecule name: 1uM Cy5-PDS + 3uM BMVC
dna type: ssDNA
array treatment: 100mM KCl
|
| Treatment protocol |
Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation. Binding experiments were then performed as previously described in Ray et al. ACS Chem Bio 2020.
|
| Extracted molecule |
other |
| Extraction protocol |
N/A
|
| Label |
Cy5
|
| Label protocol |
Synthesis of Cy5-labeled pyridostatin (Cy5-PDS) is described in (Ray et al., 2020).
|
| |
|
| Hybridization protocol |
Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with small molecules. The binding reactions (Cy5-PDS, Cy5-PDS+BMVC, or Cy5-PDS+PDS) were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS. Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.
|
| Scan protocol |
Molecule-bound microarrays were scanned with the G5761A SureScan Dx Microarray Scanner System (Agilent) to detect Cy5 signal at two laser settings (30 and 100PMT) to ensure signal intensities were below saturation. Spot intensities from microarray images were extracted using the Agilent Feature Extraction Software and are reported as raw fluorescence units. Microarrays with the fewest number of saturated spots were used for further analysis.
|
| Description |
1uM Cy5-PDS + 3uM BMVC G4 array experiment, ssDNA + 100mM KCl
|
| Data processing |
An intensity value was calculated for each target sequence by computing the median signal intensity across probes containing an identical probe identifier (ProbeID)
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Desiree Tillo |
| E-mail(s) |
desiree.tillo@nih.gov
|
| Phone |
+1-240-760-7289
|
| Organization name |
NIH/NCI
|
| Street address |
41 Center Dr, Room D310
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL28372 |
| Series (1) |
| GSE148419 |
Custom DNA microarrays reveal the selective recognition of BMVC to MYC promoter G-quadruplex: a large-scale assessment of ligand binding selectivity |
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